The architectural organization of nucleic acids and cognate factors in subnuclear microenvironments is linked with gene regulation, replication and repair (Stein, G. S., et al., Cancer Res. 60, 2067-2076 (2000); Stein, G. S. et al., J. Cell Sci. 113, 2527-2533 (2000); Lemon, B. & Tjian, R., Genes Dev. 14, 2551-2569 (2000); Dundr, M. & Misteli, T., Biochem J 356, 297-310 (2001); Iborra, F. J. & Cook, P. R., Curr. Opin. Cell Biol. 14, 780-785 (2002); Spector, D. L., Annu. Rev. Biochem 72, 573-608 (2003); and Stein, G. S. et al., Trends Cell Biol. 13, 584-592 (2003)). Spatio-temporal changes in this subnuclear organization accompany cell cycle progression and cell differentiation (Ma, H. et al., J. Cell Biol. 143, 1415-1425 (1998) and Francastel, C., et al., Nat. Rev. Mol Cell Biol. 1, 137-143 (2000)). Perturbations in subnuclear organization have been functionally related with compromised gene expression that accompanies the onset and progression of disease. See Dyck, J. A, et al., Rapid diagnosis of acute promyelocytic leukemia by immunohistochemical localization of PML/RAR-alpha protein, Blood. 1995 86(3):862-867; Karpuj, M. V., et al., Transglutaminase aggregates huntingtin into nonamyloidogenic polymers, and its enzymatic activity increases in Huntington's disease brain nuclei, Proc Natl Acad Sci USA. 1999 Jun. 22; 96(13):7388-7393; McNeil, S., et al., The t(8;21) chromosomal translocation in acute myelogenous leukemia modifies intranuclear targeting of the AML1/CBFalpha2 transcription factor, Proc Natl Acad Sci USA. 1999;96(26):14882-7.
Biological control of gene expression has previously been studied by the identification and characterization of promoter elements and their cognate regulatory and co-regulatory proteins, as well as by mechanistically defining the dynamics of chromatin structure and nucleosome organization. Results of such studies have shown that regulatory parameters of gene expression are operative within a higher-order subnuclear organization of nucleic acids and regulatory proteins. Observations made by epifluorescence and confocal microscopy have provided the initial insight into assembly of nuclear microenvironments that support the combinatorial compartmentalization of regulatory factors and chromosomal domains. Quantitative methods are needed to mechanistically associate the subnuclear organization of regulatory factors with biological control.